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Merge branch 'master' into 9766-register-workflow
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
arvjob.py
diff --git
a/sdk/cwl/arvados_cwl/arvjob.py
b/sdk/cwl/arvados_cwl/arvjob.py
index 00355973bd6c6e1416fa3e96480c96771bdc3227..a688469634bf31a20b6cf8cff5ede456277a21c4 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvjob.py
+++ b/
sdk/cwl/arvados_cwl/arvjob.py
@@
-51,7
+51,7
@@
class ArvadosJob(object):
if p.type == "CreateFile":
script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
if p.type == "CreateFile":
script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)
- script_parameters["task.env"] = {"TMPDIR":
"$(task.tmpdir)"
}
+ script_parameters["task.env"] = {"TMPDIR":
self.tmpdir, "HOME": self.outdir
}
if self.environment:
script_parameters["task.env"].update(self.environment)
if self.environment:
script_parameters["task.env"].update(self.environment)
@@
-227,7
+227,7
@@
class RunnerJob(Runner):
logger.info("Submitted job %s", response["uuid"])
if kwargs.get("submit"):
logger.info("Submitted job %s", response["uuid"])
if kwargs.get("submit"):
- self.pipeline = self.arvrunner.api.pipeline_instances().create(
+ self.
arvrunner.
pipeline = self.arvrunner.api.pipeline_instances().create(
body={
"owner_uuid": self.arvrunner.project_uuid,
"name": shortname(self.tool.tool["id"]),
body={
"owner_uuid": self.arvrunner.project_uuid,
"name": shortname(self.tool.tool["id"]),